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| Status |
Public on Mar 14, 2018 |
| Title |
Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Pancreatic endocrine lineages are derived from pancreatic progenitors that undergo a cell fate transition requiring a switch from low to high Ngn3 expression. However, the underlying chromatin regulatory mechanisms are unclear. Here, we performed epigenomic analysis of gene regulatory loci featuring histone marks in cells with low or high level of Ngn3 expression. In combination with transcriptomic analysis, we discovered that in Ngn3-high cells, the removal of H3K27me3 was associated with the activation of key transcription factors and the establishment of primed and active enhancers. Deletion of Jmjd3, a histone demethylase for H3K27me3, at the pancreatic progenitor stage impaired the efficiency of endocrine cell fate transition and thereafter islet formation. Curiously, single-cell RNA-seq revealed that the transcriptome and developmental pathway of Ngn3-high cells were not affected by the deletion of Jmjd3. Our study indicates sequential chromatin events and identifies a crucial role for Jmjd3 in regulating the efficiency of the transition from Ngn3-low to Ngn3-high cells.
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| Overall design |
The overall goal of this study was to understand the process of pancreatic endocrine cell specification and the chromatin regulations of endocrine cell fate transition. Specifically, we performed RNA-seq analyses on Ngn3-low and Ngn3-high cells from E13.5 Ngn3-GFP pancreata, and on nascent β-cells from E17.5 Ins1-RFP pancreata. To study the dynamic changes in the promoter and enhancer landscape during endocrine fate transitions, we performed ChIP-seq of promoter related histone modifications (H3K27me3 and H3K4me3) and enhancer related histone modifications (H3K4me1 and H3K27ac) in purified Ngn3-low, Ngn3-high and nascent β cells. To investigate the occupancy of NeuroD1 in endocrine progenitors, we performed NeuroD1 ChIP-seq of E14.5 whole pancreatic cells. To test the role of a histone demethylase, Jmjd3, in regulating endocrine lineage specification, we analyzed single-cell transcriptomes of Ngn3-low and Ngn3-high cells from Jmjd3-deleted pancreas.
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| Contributor(s) |
Yu X, Qiu W, Yang L, Li L, Zhang Y |
| Citation(s) |
29559448 |
| |
| Submission date |
Jul 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cheng-ran Xu |
| Organization name |
Peking University
|
| Department |
School of Basic Medical Sciences
|
| Street address |
NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA
|
| City |
Beijing |
| State/province |
- |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (258)
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| Relations |
| BioProject |
PRJNA328935 |
| SRA |
SRP078420 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84324_Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz |
582.5 Kb |
(ftp)(http) |
TXT |
| GSE84324_Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_RPKM.txt.gz |
430.6 Kb |
(ftp)(http) |
TXT |
| GSE84324_H3K27ac_Ins1-positive.bedgraph.gz |
227.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K27ac_Ngn3-high.bedgraph.gz |
191.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K27ac_Ngn3-low.bedgraph.gz |
217.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K27me3_Ins1-positive.bedgraph.gz |
256.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K27me3_Ngn3-high.bedgraph.gz |
222.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K27me3_Ngn3-low.bedgraph.gz |
203.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me1_Ins1-positive.bedgraph.gz |
327.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me1_Ngn3-high.bedgraph.gz |
328.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me1_Ngn3-low.bedgraph.gz |
268.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me3_Ins1-positive.bedgraph.gz |
39.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me3_Ngn3-high.bedgraph.gz |
145.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_H3K4me3_Ngn3-low.bedgraph.gz |
105.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_Input_E14.5.bedgraph.gz |
144.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_Input_Ins1-positive.bedgraph.gz |
287.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_Input_Ngn3-high.bedgraph.gz |
345.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_Input_Ngn3-low.bedgraph.gz |
302.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_NeuroD1_E14.5.bedgraph.gz |
65.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE84324_Single-cell_RNA-seq_Gene_RPKM.txt.gz |
5.2 Mb |
(ftp)(http) |
TXT |
| GSE84324_Single-cell_RNA-seq_Gene_Read_Count.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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